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Even commonly used housekeeping genes may exhibit circadian oscillations, which can confound rhythmic gene expression analyses and hinder biomarker identification. To address this limitation, we evaluated the gene expression stability of 11 commonly used housekeeping genes in blood collected every 6 h over 24 h period from 40 adults with varying OSA severity and controls. Stability ranking by analytical tools RefFinder and EndoGeneAnalyzer identified ACTB (\u03b2-actin) and RPL13A (ribosomal protein L13a) as the most consistent reference genes, with minimal intra- and inter-individual variability across sampling times and disease groups. Their suitability was assessed by personalized cosinor analysis of core clock genes (BMAL1, PER2, CRY1), demonstrating that appropriate normalization enables detection of circadian oscillations in clinical samples. Using the optimal normalization, CosinorPy analysis of the core clock genes revealed significant circadian oscillations of at least one clock gene in the studied participants. These findings establish ACTB and RPL13A as robust reference genes for blood-based circadian studies of OSA and provide an important methodological framework for future circadian biomarker research.<\/jats:p>","DOI":"10.3390\/biom16071013","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T16:30:37Z","timestamp":1783701037000},"page":"1013","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Reference Genes for Circadian Profiling of Core Clock Genes in the Blood of Obstructive Sleep Apnea Patients"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7796-1585","authenticated-orcid":false,"given":"Katarina","family":"Nahtigal","sequence":"first","affiliation":[{"name":"Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5135-3752","authenticated-orcid":false,"given":"Ana","family":"Halu\u017ean Vasle","sequence":"additional","affiliation":[{"name":"Computational Biology Group, Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4735-2025","authenticated-orcid":false,"given":"Tinkara","family":"Kreft","sequence":"additional","affiliation":[{"name":"Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2601-2291","authenticated-orcid":false,"given":"Cene","family":"Skubic","sequence":"additional","affiliation":[{"name":"Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miha","family":"Mraz","sequence":"additional","affiliation":[{"name":"Computational Biology Group, Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4600-1730","authenticated-orcid":false,"given":"Miha","family":"Mo\u0161kon","sequence":"additional","affiliation":[{"name":"Computational Biology Group, Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4609-8318","authenticated-orcid":false,"given":"Leja","family":"Dolenc Gro\u0161elj","sequence":"additional","affiliation":[{"name":"Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damjana","family":"Rozman","sequence":"additional","affiliation":[{"name":"Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1764","DOI":"10.1038\/s41598-022-05836-1","article-title":"Evaluation of Stable Reference Genes for qPCR Normalization in Circadian Studies Related to Lung Inflammation and Injury in Mouse Model","volume":"12","author":"Giri","year":"2022","journal-title":"Sci. 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